1NVM

Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate

Structural Biology Knowledgebase: 1NVM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NVM

Classification: LYASE / OXIDOREDUCTASE

Total Structure Weight: 285363.81

Macromolecule Entities
Molecule Chains Length Organism Details
4-hydroxy-2-oxovalerate aldolase A, C, E, G 345 Pseudomonas sp. cf600 EC#: 4.1.3 IUBMB
Gene Name(s): dmpG
acetaldehyde dehydrogenase (acylating) B, D, F, H 312 Pseudomonas sp. cf600 EC#: 1.2.1.10 IUBMB
Gene Name(s): dmpF

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAD
Query on NAD

B, D, H NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A, B, C, E, G (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, C, E, F, G SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXL
Query on OXL

A, C, E, G OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, C, E, G MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.189
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.20 α = 90.00
b = 140.00 β = 90.00
c = 191.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-04
  • Released Date: 2003-06-17
  • Deposition author(s): Manjasetty, A.B., Powlowski, J., Vrielink, A.

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4